Re: [R] Tool for update
Hello, Am Mittwoch, 23. März 2005 06:12 schrieb Yuandan Zhang: Hi, Is there any tool to check if there is update version of a package available? I look for things alike YUM for linux? Start R --no-save on a root console and launch update.packages() from within R-Enviroment. Surely, this is not like YUM but does a supherb job. Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Clustering of Binary data in R
Hello, Am Freitag, 4. März 2005 15:51 schrieb sima fakheran: Good afternoon! I would like to ask you about similarity measures and clustering in R for Binary data. Would you please kindly help me and let me know about that commands in R? help.seach(cluster) will give you an overview of available appropriate functions in your local R installation. In these help pages you'll find some very good examples on how to do clustering. If you want some more detailed response have a look at the posting guide (www.r-project.org/posting-guide.html) and provide some more informations on your data and what you've done so far (example code)! Another source of wealth is the Mail archive of this R-help, which provides a helpful search dialog to browse regards Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running out of memory
Hello, Am Mittwoch, 16. Februar 2005 20:48 schrieb Stephen Choularton: Hi I am trying to do a large glm and running into this message. Error: cannot allocate vector of size 3725426 Kb In addition: Warning message: Reached total allocation of 494Mb: see help(memory.size) Am I simply out of memory (I only have .5 gig)? Is there something I can do? This question has been answered a hundred times on this list. The best idea is trying to search for memory datasets in the lists mail archive . Which gives you 246 hits! Please give some more information on what system are you using (32, 64 bit) etc. Regards Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] switching to Linux, suggestions?
Hello, Thomas W Volscho schrieb: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? R is developed on Linux, so there shouldn't be too much restrictions on whatever distri you're going to use! If running a new shiny Desktop you might consider other aspects than using R, which should run with every Linux distribution. If you're looking for something comfortable to install and maintain you might give Quatian a try (http://dirk.eddelbuettel.com/quantian.html). This is a somewhat modified Knoppix trimmed to statistical analysis (not entirely, though) regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Protocol for answering basic questions
Hello, Liaw, Andy schrieb: Apologies to those who are tired of these rather off-topic discussions. I'll try to be brief. I will toss in my perspective, instead of speaking for others. To me, it's not how basic the questions are, but how they are being asked. It's been pointed out by several people: If you showed some effort in trying to solve the problem yourself (by describing what you have tried and how that failed), you will almost always get useful replies without being chastised. Those who received less than enthusiastic responses are generally those that do not show any apparent efforts in trying to solve the problem themselves. As been said ad nauseam before, R is a purely volunteer-based project, and people on this list help others out of their good will. It's rude and discourteous to abuse that. It's OK if you need some spoonfeeding (I need that quite often myself), but at least show how you have tried to use the spoon yourself, instead of just showing us your open mouth. Even if you did , but missed to get a look at R FAQ and other resources, you're pointed at the appropriate issue! I think that's quite okay with me! Well its not only a question of either getting a RTFM or being just ruffled by someone. AFAIR I sometimes got both..well that okay, and teaches you some decency regarding what questions might be raised to bother generally helpful people on this list. BTW, that's also a prime example of how `gentle' R-help is compared to most other lists. I suspect those whose egos are buised by responses to their questions probably haven't had much experience with mailing lists. There are many lists which don't give a dam about postings containing no meaningful subject or a proper description of your problem. It stunning to see that some people even don't care to make up their minds related to this issue (well, maybe only to the point when they start using the mail archive and give up on browsing too many no subjects-mails. Well, basically I am agree to your statement, Andy! Also, I think it should be made clear that the R user community is (much?) larger than those who subscribe to R-help/R-devel/R-*/BioC lists. I know many who use R as their primary tool, yet do not subscribe to R-help. These people managed to get by just fine, either with help pages/manuals/books, or more experienced colleagues. Hmm, maybe that is the hardcore way of doing things. I am sure there are lots of people who like this learning method, but not quite sure if this the majority With regard to this I (still) think that using R demands some far reaching skills, i.e. not entirely restricted to profound knowledge in statistics, but also related to OO programming. If you never did any programming even help pages, manuals and books are of limited usefulness. So, it takes time to get into and not all of your problems might me solved soon...hmm, where is this damned..heh...my..spoon... ah . Well to all beginners, like me, it takes time and some efforts to get into, sure that this investment will sum up to something good. I can recommend the mail archive of R-help, since I am sure that nearly almost (all) of my stupid beginners questions are already answered (beware this may only correct for a= 0.05 CI), the rest is found in R FAQ.. sincerely Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SAS or R software
Hello, BXC (Bendix Carstensen) schrieb: Two major advantages of SAS that seems to have been overlooked in the previous replies are: 1) The data-set language is SAS for data manipulation is more human-readable than R-code in general. R is not a definite write-only laguage as APL, but in particular in datamanipulation it is easy to write code that is impossible to decipher after few weeks. Not quite sure if this is a valid point! Mostly you'll have to comment on code as it is taught in programming course. If your comments are clear, there shouldn't be any problems to understand your code after weeks , month or maybe... Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Power sampling
Hello Uwe, Uwe Ligges schrieb: Thomas Schönhoff wrote: You have to tell us for which test you are going to calculate the power ... (and there might be nothing, since calculating the power precisely is not always that easy). Given my example from the first message I asked for a function which enables me to calculate a reasonable sample size. I don't know the true mean or standard deviation of the population, I only know: n= 5.000.000 observations over 70 variables determined alpha = 0.01 I want to know how to generate a sufficiently sized sample based upon above mentioned facts to make some valid predictions regarding my population. All I can hink of for now is that a two-tailed power test is required to find out if H0= random effect or H1= no random effect hypothesis is accepted/rejected. In epidemiological studies this situation is described like this: How many cases do I have to include in my sample (s) to gain some representative results from a unknown population (=true mean, std-deviation etc.)? How can I approach a situation like this in R ? Regards Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.1 year 2004 month11 day 15 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
Tim Cutts schrieb: Any GUI to R could (and should) be able to store the command line equivalent to what it has just done, to satisfy the reproducible criterion above, but I suspect it could still lead to some pretty shoddy work being done by careless and lazy scientists, and we get enough of that already. In that respect you should have a look at Emacs/XEmacs/ESS package. This package combines the power of command line and reproducibility of what has been done to generate graphs or whatever you like. Its also equipped with a nice ref-card-pdf which is very helpful to learn common shortcuts to increase your productivity levels. I wouldn't call ESS necessarily a GUI in a traditional sense, though. When I started using R I was inclined to use the RCommander-GUI. After fiddling with this for a while I came to the conclusion that its possibilities are, at least for the moment, really limited. Furthermore some things increased my irritation levels, i.e. orientation to push the correct buttons to achieve a specific task. If I hit a false button I hardly wasn't able to find out what actually went wrong. Nevertheless, for me as a beginner in GNU R, who never used S before, but primarily SPSS and BMDP in early times, it is a long way to gain some control of advanced aspects of using R. This is also true despite the fact that I took statistics courses for several years and do have experiences in research projects (social sciences and epidemiology), so I'll would agree that using GNU R has some hidden costs for me! To sum up, what I am in need to is an extensive example based help-system, focused on how to do things in R. In parts this is already there, i.e. SimpleR from Verzani (contributed docs area) etc. Hopefully I can contribute to this in future, since it is seems to me invaluable to learn R by going through example-based lessons (some are found in vignette() ). These are much more comprehensible to me than those short reference like entries in the current help-system, mostly due to their very technical approach (same is to be said about the official GNU R manuals, especially The R Language, which wasn't a great help for me when I took my first look at GNU R). In this context something like the GuideMaps of Vista come to my mind! But to be as clear as possible, I think GNU R is great and I appreciate all the efforts done by the R core team and associates! Nevertheless it seems to be valuable to re-think the help-system in R with respect to those who may have a good understanding in statistics, but lacking some basic experiences in how to introduce themselves to sophisticated world of R/S languages. Regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Power sampling
Hello, after a unsuccessful search in lists maliarchive I wonder how I could estimate the power of a sample size related to an unknown population. Given the following (fake))situation: I do have a database containing about 5 millions observations over 70 variables. I would like to compute (as epidemiologists are used to) the required size of a sample to do some test on a test sample (test data), later doing some subsequent analysis of a new sample to build a prediction model. Help facilities of R show some entries regarding power, but none of them seemed to be appropriate for my purpose (maybe I am wrong, but sometimes I have some difficulties to decipher the message of those tiny hints for available packages) I would appreciate somebody effort to point me to the right package/function to archieve this task! regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Using GNU R on a two box cluster
Hello, right now I'm thinking about running R 2.0.0 on box A (Debian SID) but at the same time having access to the ressources of box B (Ubuntu Linux) regarding disk capacity, RAM, idle CPU cycles . Is there anyone of you that has already installed and administred such a tiny (home based) cluster? Well, the term cluster seems quite a bit of an exaggeration related to what I am looking for! I am absolutely new to this subject and I would appreciate some hints on where to start doing such things with my GNU R on both boxes. Maybe a pointer too some introductory materials focussed to doing clustering stuff with GNU R would be sufficient. Are there any recommended methods or tools to realize a two nodes cluster? regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error message from vignette strucchange-intro example
Hello, I am just studying the following example from vignette: strucchange-intro, contineousely ending up in an error. This is the given code: 1. library(strucchange) 2. data(USIncExp) 3. if (!package:stats %in% search()) library(ts) 4. USIncExp2 - window(USIncExp, start = c(1985, 12)) A.Modelling: coint.res - residuals(lm(expenditure ~ income, data = USIncExp2)) coint.res - lag(ts(coint.res, start = c(1985, 12), freq = 12),k = -1) USIncExp2 - cbind(USIncExp2, diff(USIncExp2), coint.res) USIncExp2 - window(USIncExp2, start = c(1986, 1), end = c(2001,2)) #here is what eval is looking for in vain: diff.expenditure colnames(USIncExp2) - c(income,expenditure,diff.income,diff.expenditure,coint.res) B. Error correction formula ecm.model - diff.expenditure ~ coint.res + diff.income C. Using EFP (OLS) test function ocus - efp(ecm.model, type = OLS-CUSUM, data = USIncExp2) or me - efp(ecm.model, type = ME, data = USIncExp2, h = 0.2) Both commads under C give me : --- Error in eval(expr, envir, enclos) : Object diff.expenditure not found --- Since quite some time I am sitting here and wonder whether there is an error in the given code or if it my simple inability to catch up with a self-breed error (???) -- platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R Maybe someone to direct my delusion to something helpful, so far I've looked for typos and alike, as far I can say the code should work, isn't it? Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Revision: post on Intro to R lecture
Hi, Arin Basu schrieb: This follows my earlier post on webized slides on lecture presentation on introducing R. I learned that in Mozilla (Firefox) browsers, the slides did not show up. Sorry for the no show. As a reluctant windows user, I kind of carelessly clicked through Powerpoint to convert the presentation file to its html form, unwittingly leading to the mess. See if it got corrected now (I do not have firefox yet in my computer, so no way of knowing whether it works), and please let me know. Also, made some changes and reformatted the original slides to make them other browser compatible, thanks to comments from Gabor Grothendiek, Stuart Lesk, and Sundar Dorai-Raj. Here is the URL again: http://www.aloofhosting.com/arinbasu/Rintroweb.htm I'm agree to Clints posting, much improved and now readable. Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can't load rgl library
Hello, [EMAIL PROTECTED] schrieb: Hi, I've installed rgl package through R CMD INSTALL on a Debian-Sarge machine (PIV) without any compiling error (see attached file), but when trying to load this package within R (and also Rcmdr library) I get: library(rgl) RGL: GLX extension missing on server Error in firstlib(which.lib.loc, package) : error rgl_init error in library(rgl) : .First.lib failed Segmentation fault Sounds like you're missing opengl/ xlibmesa(gl) +(glut) packages; make sure that these packages are installed and work flawlessly. HtH __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can't load rgl library
Hello, [EMAIL PROTECTED] schrieb: Hi, I've installed rgl package through R CMD INSTALL on a Debian-Sarge machine (PIV) without any compiling error (see attached file), but when trying to load this package within R (and also Rcmdr library) I get: library(rgl) RGL: GLX extension missing on server Error in firstlib(which.lib.loc, package) : error rgl_init error in library(rgl) : .First.lib failed Segmentation fault Same failure problem if I use the apt option (apt-get install r-cran-gl). I've searched through the R mail archives but couldn't find or understand the answer for this problem. I just forgot to say that you also could try to rename /usr/share/tls (IIRC, its tls directory!) to /usr/share/tls_old and re-try loading the package. Maybe default installation doesn't recognize the working drivers, especially if you run NVidia driver on your box! HtH __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to set options (variables) permanently
Hi, after starting Emacs/ESS/R environment I tried to launch edit or fix. This normally should fire up the $editor, isn't it. Instead of this I regularily I run into an error that there something wrong with $editor. --- op - options(); str(op) Amongst many entries you'll find this: $ editor : chr emacsclient Seems to be plain obivious that this command (instead of 'emacs' or '/usr/bin/emacs') would never run. So an options(editor=emacs) does the trick, I already found out.. But it is very uncomfortable to set the $editor variable every time when you return to R! I've tried to achieve this by: save.image() or q(yes) and also: options(OPT = emacs) options(EDITOR=emcas) but this didn't work! Next time I fired up Emacs/ESS/R again, the $editor variable is still defaulting to emacsclient?! Is there any possiblity to adjust and store this variable (and others) permanently ? My search on this topic in R-Mailing-Archives failed. regards Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] fix and edit don't work the expected way
Hello, I am tinkering a bit with options(), namely, how to query and set them up to suit my needs. 1) The basic problem seems that the editor entry in options looks like this: options() - $editor [1] emacsclient - After setting this option to /usr/bin/emacs by doing: options(editor=/usr/bin/emacs) I try to run fix(fun) or edit(fun) and run into this error: - Error in edit(name, file, editor) : An error occurred on line 17 use a command like x - edit() -- This error is also noticed when loading the function into edit()/fix(), doing some changes and trying to save these modifications too tmp buffer. 2) Furthermore I try to set the $editor option not only for current but also for future session!? It seems like that I run regularily into troubles starting $editor(emacsclient) from within Emacs/ESS/R enviromnent. How to do that? I've read in FAQ that local copies of .Options are quietly disregarded at start up. So I started looking at the global one in /etc/R/Renvir directory and also tried : -- save.image() - But this wasn't of much help to store the $editor variable on the long run! (Since I am at the beginning of my exploration of R I didn't want to mess up the whole system configuration by doing some modifications to this file) Obviousely, I don't do it correctly, but I can't figure out whats wrong? Anyone help is appreciated. Thanks Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu (Debian) system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R Emacs2121.3+1-7 ESS5.2.2-2 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] debugging functions within Emacs/ESS/R
Hi, I currently following some introductory material Data mining with R, which was highly reccommended to me (its really great!). During my studies I tried to run a given function to identify and substitute unknown values. Seemingly, running this function (page 57) did not work and gives me an error message. It would be very easy just to copy and paste this function to ask for help on this list. Guess' that most afficiandos on this list need a simple glimpse to tell me whats wrong, but I am more interested in learning how to debug buggy functions within Emacs/ESS/R by myself! Reading FAQ, ?debug, ?traceback, ?recover, ?browse help files didn't prove to be a good starting point for me (sorry, my programming skills are somewhat limited at the moment). Is there any learning-by-doing example of debugging functions in Emacs/ESS/R I may have not noticed now? Thanks Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] WARNING: terminal is not fully functional
Hello, first trials to run R from inside of Emacs repeatedly gives me: ?sink WARNING: terminal is not fully functional - (press RETURN) - Seems like this is going to happen to all help calls using a questionmark! Any idea how to change this, maybe this isn't subject to change at all!??? Thanks Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R And: emacs2121.3+1-7 ess5.2.2-2 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] library functions looks up wrong directory
Hello, I just encountered this error from within R: -- library() Warning message: library '/usr/local/lib/R/site-library' contains no package in: library() --- which is basically correct since all the looked up packages are in /usr/lib/R/site-library, not in /usr/local Now I am looking for a possibility to adjust my config too /usr/lib/R/site-library. Is there a special config file to do this in R ? platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major1 minor9.1 year 2004 month06 day 21 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loading error of the Rcmdr library on Debian Sid
Hello, A.J. Rossini schrieb: You can apt-get RGL in sid. An apt-cache search or (Synaptic search) RGL gives me r-cran-rgl 0.64.13-1. This package is already installed! regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Howto enlarge fonts size in R- Graphics?
Hi, I am fairly new to GNU R ! At the moment I am doing an intensive learning on the basics of GNU R-1.91, especially graphics like plots and alike, by reading the introductory docs! Well, except some occasional glitches (X11 output errors) everything seems to be fine, thanks to developers for this fine program! But there is a slight problem with the size of fonts in graphics, i.e. its very hard form me to read labels of variables in plots or other graphical representations! (yes, I am little short sighted) How may I mainpulate/enlarge the fonts size in graphics from within GNU R ? Thanks for your time Thomas System: GNU/Linux (Debian Sid) GNU R: 1.91 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Howto enlarge fonts size in R- Graphics?
Hello, Thomas Schönhoff wrote: Well, thanks, I'll have a look at your advices. regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
